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Mol Path Part 1 2022 > Variants I Need to Learn > Flashcards

Variants I Need to Learn Flashcards

1
Q

What is the ISCN for the EWSR1-FIL1 fusion seen in Ewing Sarcoma?

A

t(11;22)(q24;12)

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2
Q

What is the ISCN for the BCR-ABL1 fusion

A

t(9;22)(q34;q11.2)

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3
Q

Whats is the ISCN for the RUNX1-RUNX1T1 fusion?

A

t(8;21)(q22;q22.1)

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4
Q

What is the ISCN for CBFB-MYH11

A

inv(16)(q13;q22) or t(16;16)(q13;q22)

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5
Q

What is the ISCN for MLLT3-KMT2A?

A

t(9;11)(p21;q23)

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6
Q

What is the ISCN for DEK-NUP214?

A

t(6;9)(p23;q34.1)

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7
Q

What is the ISCN for KAT6A-CREBBP?

A

t(8;16)(p11;p13)

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8
Q

What is the ISCN for GATA2, MECOM?

A

inv(3)(q21;q26) or t(3;3)(q21;q26)

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9
Q

What is the ISCN for the IGH-BCL2 rearrangement seen in 90% of follicular lymphomas?

A

t(14;18)(q32;q21)

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10
Q

What is the iSCN for the IGH-CCND1 rearrangement typically found in Mantle cell lymphoma?

A

t(11;14)(q13;q32)

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11
Q

What is the iSC for the IGH-MYC rearrangement found in 80% of Burkitt lymphoma cases?

A

t(8;14)(q34;q32)

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12
Q

What is the ISCN for the PAX3-FOXO1 and PAX7-FOXO1 rearrangements identified in rhabdomyosarcoma?

A

PAX3-FOXO1 - t(2;13)(q35;q14)
PAX7-FOXO1 - t(1;13)(p36;q14)

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13
Q

What is the ISCN for the SS18 rearrangement typically seen in synovial sarcoma and what genes can be involved?

A

t(x;18)(p11.2;q11.2)
Chromosome 18 - SS18
Chromosome x can be SSX1, SSX2 or SSX4

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14
Q

What is the ISCN for the FUS-DDIT3 fusion characteristic of myxoid liposarcoma?

A

t(12;16)(q13;q11)

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15
Q

What is the ISC for the EWSR1-ATAF1 rearrangement seen most frequently in clear cell sarcoma?

A

t(12;22)(q13;q12)

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16
Q

What is the ISCN for the TCF-PBX1 fusion which is associated with a poor prognosis in ALL?

A

t(1;19)(q23;p13)

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17
Q

What is the ISCN for the TLF-HLF fusion which is associated with a poor prognosis in ALL?

A

t(17;19)(q22;q13)

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18
Q

What is the ISCN for the ETV6-RUNX1 fusion which is associated with a good prognosis in ALL?

A

t(12;21)(p13;q22)

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19
Q

What is the ISCN for the IGH–BCL2 rearrangement seen in 90% of follicular lymphoma?

A

t(14;18)(q32;q21)

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20
Q

What is the ISCN for the IGH-CCND1 rearrangement identified in Mantle Cell Lymphoma?

A

t(11;14)(q13;q32)

21
Q

What is the ISCN for the IGH-MYC rearrangement identified in 80% of Burkitt lymphoma?

A

t(8;14)(q34;q32)

22
Q

What is the ISCN for the IGH-FGFR3 fusion which is associated with a poor prognosis in multiple myeloma and Smouldering Multiple Myeloma?

A

t(4;14)(p13;q32)

23
Q

What genomic change is seen in 90% of Waldenstrom marcoblobulinemia and can be used to rule out marginal zone/MALT lymphoma?

A

MYD88 L265P

24
Q

Mutations in what gene cause resistance to Ibrutinib for the treatment of Waldenstroms marcoglobulinemia?

A

CXCR4

25
Q

What is the ISCN for PML-RARA?

A

t(15;17)(q24.1;q21.2)

26
Q

What is the most common MPL mutation seen in MPN?

A

W515L/K

27
Q

What mutation occurs in the majority of systemic mastocytosis cases?

A

KIT D816V

28
Q

What are the four TPMT deficiency alleles which account for 95% of TMPT deficiency cases?

A

o TPMT 2* (238G>C) – 100x decrease in activity (very low)
o TPMT *3A (contains two SNPs, *3B and *3C) – No detectable enzyme activity
o TPMT *3B (460G>A) – 4x decrease in activity (very low)
o TPMT *3C (719A>G)) – 1.4x decrease in activity

29
Q

What are the four clinically relevant DPYD variants and their associated impact on DPD function?

A

o c.1905+1G>A, activity 0
o c.1679T>G, activity 0
o c.2846A>T, activity 0.5
o c.1129-5923C>G (c.1236G>A), activity 0.5

30
Q

What variant is in perfect linkage disequilibrium with the DPYD c.1129-5923C>G variant?

A

The synonymous variant c.1236G>A
This can be used as a proxy when testing

31
Q

What are the hotspots of GNAQ and GNA11 in uveal melanoma?Varin

A

Exons 4 & 5
Codons Q209 and R183

32
Q

What proportion of GIST tumours have a KIT or a PDGFRA variant?

A

KIT - 80%, PDGFRA 10%

33
Q

What proportion of idiopathothic eosinophilia cases have a FIP1L1-PDGFRA fusion?

A

10-20%

34
Q

What are the time frames for analysis of a ctDNA sample in an EDTA and a Cell Stabilisation tube?

A

EDTA - 1 hour
Cell Stabilisation -At lab within 48 hours

35
Q

What proprtion of Burkitt Lymphoma cases has the IHC-MYC rearrangement?

A

80%

36
Q

How is Burkitt-like lymphoma differentiated from Burtkittts?

A

Does not have an MYC rearrangement and as an abnormal 11q

37
Q

How is High grade B-cell lymphoma distinguished from Burkitts?

A

Also has a MYC rearrangement but additionally has a BCL2 and/or BCL6 rearrangement

38
Q

What proportion of WM (MYD88+ and -ve) has a CXCR4 variant?

A

35% of cases with MYD88, 5% MYD88 -ve

39
Q

What lymphomas does MYD88 distinguish Waldenstrom’s from?

A

IgM myeloma (MGUS) or Marginal Zone Lymphoma

40
Q

How many copies of MDM2 is required to be considered a gain in sarcomas?

A

> 4 in 10 cells

41
Q

What diagnoses in sarcomas does MDM2 amplification help inform?

A
  • Well differentiated liposarcoma
    o. MDM2 used to differentiate from benign lipomatous tumours
  • Dedifferentiated liposarcoma
    o MDM2 used to differentiate dedifferentiated liposarcoma from high grade sarcoma.
  • Bone tumours
    o MDM2 in low grade fibrous tumour supports low grade osteosarcoma
    o MDM2 in high grade osteosarcoma supports progression from a low grade tumour.
42
Q

What is charactertistic of well differentiated liposarcoma?

A

o Characterised by giant marker and/or supernumery ring chromosomes, both of which contain multiple copies of MDM2.

43
Q

What proportion of colorectal cancers have KRAS, NRAS and BRAF V600E variants?

A

KRAS - 40%
NRAS - 5-8%
BRAF V600E - 5-9%

44
Q

e) What enzymes are used in DNA extraction?

A
  • Protease – denature proteins (Proteinase K)
  • RNAase – Removed traces of RNA in a DNA extraction
  • DNAse – Removes traces of DNA in an RNA extraction
  • Lytic enzymes – Cell lysis (many types, e.g. Lysozyme)
45
Q

d) What are the major components of extraction buffer?

A
  • Tris, EDTA, NaCl, sodium lauryl and SDS.
46
Q

f) What are the types of DNA damage caused by DNA fixation?

A
  • Crosslinks
  • Fragmentation
  • Abasic Sites
  • Deamination of Cytosine Bases (cytosine -> Uracil)
47
Q

g) What stain is used to analyse histology of a cell?

A
  • H&E – Haematoxylin (ribosomes, chromatin (genetic material) deep blue colour) and Eosin (cytoplasm, collagen, connective tissue, orange-pink-red)
48
Q

In which tumour types does MGMT have prognostic implications and therapeutic implications

A

Prognostic - Gliomas & Glioblastoma
Therapeutic - Glioblastoma

49
Q

What is the IDH1 hotspot seen in gliomas and what proprtion of IDH mutations does it account for?

A

R132H - 90%

Mol Path Part 1 2022 (7 decks)

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